[gmx-users] question regarding restraints

[gurpreet singh]

Thanks David for your quick reply

you were write actually , there is no energy term corresponding to the
postional restrain in the log file,

but i am using the proper posre.itp file created by genpr command (restrain
for whole protein) ,

genpr -f 4min_ion_water.pdb -o posre.itp -fc 50

then i have included define also in my .mdp file corresponding to this
restrain file
i used grompp in the following way

grompp -f 6eq_w.mdp -c 5min_w.gro -p aquapo_grom.top -r posre.itp -o
6eq_w.tpr

then what else i should check to rectify this problem ?


{ Actually my protein is a dimer, earlier two .itp files were crested by
pdb2gmx in the beginning but to reduce the restrain and to include all the
hydrogens added this time in the restrain file i made another .itp file.}


With regards
Gurpreet
On 7/21/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> gurpreet singh wrote:
> > Hello users
> >
> > I am using the gromacs 3.3 with 43a1 force field.
> > I am using a restraint force of 50 intially during the beginning of
> > protein simulation in water, even after such a high value of restraint
> > force i can see some major deviations in my structure during the
> > simulation.
> >
> > My doubt is that since i am applying enough restrain force on the
> > protein it should not deviate at all from its native conformation.
> > I want to know is this the usual behavior in gromacs or i am making some
> > mistake in  applying restrain.
> >
> > I am using a posre.itp file using define = -dposre in the .mdp file for
> > applying the restraining force.
> >
>
> are you sure the restraints are applied? check whether you have an
> energy term corresponding to it. typical force constants people use are
> 1000 kJ/mol/nm^2
>
> >
> > With regards
> > Gurpreet
> >
> >
> >
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> >
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>
> --
> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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